Two-Scale ¹³C Metabolic Flux Analysis for Metabolic Engineering

Area of Science:

• Synthetic Biology
• Metabolic Engineering
• Computational Biology

Background:

• Accelerating the Design-Build-Test-Learn (DBTL) cycle is crucial for bioengineering organisms.
• The Learn phase uses experimental data to refine designs.
• Metabolic flux analysis provides mechanistic understanding of cellular metabolism.

Purpose of the Study:

• To provide a guide for performing metabolic flux analysis in the Learn phase of the DBTL cycle.
• To demonstrate how to convert ¹³C labeling data into cellular flux determinations.
• To direct genetic engineering strategies for metabolic engineering.

Main Methods:

• Utilizing the Joint BioEnergy Institute (JBEI) Quantitative Metabolic Modeling (jQMM) library.
• Performing ¹³C Metabolic Flux Analysis (MFA) and two-scale ¹³C MFA (2S-¹³C MFA).
• Employing Flux Balance Analysis, MoMA, and ROOM methodologies for model analysis.

Main Results:

• A step-by-step guide for metabolic flux analysis using ¹³C labeling data.
• Demonstration of the jQMM library's capabilities in predicting metabolic behavior.
• Actionable predictions for modifying cellular metabolism for bioengineering goals.

Conclusions:

• Metabolic flux analysis is a powerful tool for the Learn phase of the DBTL cycle.
• The jQMM library facilitates the conversion of experimental data into engineering strategies.
• Open-source tools like jQMM enhance reproducibility and collaboration in metabolic engineering.